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Dear all,
maybe I'm missing the point completely, but aren't we comparing apples
and pears here? What we have in this type of argument is
1. "RMSD on bond lengths"
I guess this is what we have in the PDB headers as
RMS DEVIATIONS FROM IDEAL VALUES
and what is defined in mmCIF as
_refine_ls_restr.dev_ideal
For the given parameter type, the root-mean-square deviation
between the ideal values used as restraints in the least-squares
refinement and the values obtained by refinement. For instance,
bond distances may deviate by 0.018 A (r.m.s.) from ideal values
in the current model.
See:
http://mmcif.pdb.org/dictionaries/mmcif_std.dic/Items/_refine_ls_restr.dev_ideal.html
2. the Engh & Huber set of parameters
These are given as a distribution (mean and sigma) for different
types of bonds (Table 2 in paper):
"Averages, standard deviations and standard errors were
calculated, with and without elimination of values outside four
standard deviations from the mean."
See:
http://journals.iucr.org/a/issues/1991/04/00/li0061/li0061.pdf
These two quantities are something completely different - at least as
far as I understand it. The rms deviation from the mean of a
distribution is only identical to the standard deviation of that
*same* distribution.
I don't understand why the RMSD on bond lengths should/can be compared
to the standard deviation of the Engh&Huber distributions to see if a
structure is well restrained?
If we would calculate the distribution of bond lengths within a
refined structure, we would also get a mean and a sigma. And this
could be compared to the Engh&Huber parameters, since it measures the
same thing.
However, there is some sense in arguing about well restrained
structures while looking at the RMSD on bond lengths:
- high resolution => more observations than parameters => the data
tells us what the bond-lengths should be => we can deviate from
the Engh&Huber mean values => larger rmsd(bond)
- low resolution => few observations => the data doesn't tell us
what the bond-lengths should be => we can't really deviate from
the Engh&Huber mean values (prior) => smaller rmsd(bond)
But what should be those values? I guess at 1A resolution I'd expect a
rmsd(bond) of 0.02 or larger. And at 3.5A I'd expect a rmsd(bond) of
0.005 or smaller. But these are personal choices (same as I/sig(I)
or Rmerge cut-offs in data-reduction).
But maybe I'm completely wrong here ... correct me please?
Cheers
Clemens
On Wed, Aug 23, 2006 at 09:50:04AM +0200, Fred. Vellieux wrote:
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>
>
> On Tue, 22 Aug 2006, Bernhard Rupp wrote:
>
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
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> >
> > > at the resolution you're working at the RMSD on bond
> > > lengths should be ca. 0.012, not 0.02 A.
> >
> > Interesting statement. I agree that for
> > very well determined small molecule structures, the
> > overall bond length variation is about 0.014 A or so.
> >
> > That fits quite well with what you say. It just means
> > that the structure should be restrained to reflect
> > reality.
> >
> > But: What does coordinate rmsd exactly have to do with
> > resolution? If the 3.5 A structure has 0.012 A
> > rmsd, does that mean that a 1.2 A structure
> > should have 0.005? I have a feeling that would
> > be a serious case of over-restraining.
> >
> > Should not all structures reflect the same
> > 'real world' rmsd (plus minus some minor individuality)
> > if the restraint weights are properly selected?
> >
> > Maybe the small molecule/shelxl fellows may chime in here:
> > What is the expected rmsd for a high res protein
> > structure vs. a low res? I had a feeling that
> > super low rmsd is partly abused as a sign of crystallographic
> > prowess, like building fantasy stuff into nonexistent density
> > just to have no missing residues &c &c &c...
> >
> > Thx, br
>
> Hi Bernhard,
>
> What I wrote means that unless you have superhigh resolution (in which
> case you can simply forget about library restraining --- you can
> even count the number of electrons for one atom to assign its type) the
> model should reflect reality.
>
> You state that reality is RMSD = 0.014, I thought it was 0.012 A. Small
> mistake from my part. Anyway the message was simply to state that
> targetting an RMSD of 0.02 meant that the geometry was not restrained
> tightly enough to fit what one expects at a resolution where unrestrained
> refinement cannot be done (who would attempt unrestrained refinement at
> 3.4 A refinement?).
>
> Fred.
>
> --
>
> s-mail: F.M.D. Vellieux (B.Sc., Ph.D.)
> Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
> 41 rue Jules Horowitz
> 38027 Grenoble Cedex 01
> France
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